After a 16-day government shutdown, the Defense Department is returning to the task of absorbing the steepest budget cuts in decades. And now more than ever, it appears likely the spending caps known as sequestration, which are driving major decisions across the department, are here for the long term.

“It’s important to note that Congress did not remove the shadow of uncertainty that has been cast over this department,” Defense Secretary Chuck Hagel said Oct. 17 after Congress finalized the deal to reopen the government.

That deal leaves in place the so-called Budget Control Act, the 2011 federal law that caps spending for government agencies. In effect, it will limit the Pentagon’s budget for 2014 to about $475 billion, far lower than the $526 billion President Obama requested for DoD earlier this year.

Beyond Washington, that likely means involuntary separations for thousands of troops, though the details for each service remain unclear. Also in the wind: massive cuts to training budgets, reductions in flying hours and hard choices about which weapon programs will be delayed or cut entirely, Pentagon officials say.

Lifting those defense spending caps was never really considered as part of the latest truce on Capitol Hill. Some Republican defense hawks floated the idea, but GOP leaders — mindful of their vocal tea party faction that favors sharply reduced spending — never seriously considered that as a bargaining chip.

As the dust settled from the bruising budget battle, some Republican leaders suggested that preserving those budget cuts was a victory in their eyes.

“We’re protecting the government spending reductions that both parties agreed to under the Budget Control Act,” Senate Minority Leader Mitch McConnell of Kentucky said in the final hours of the negotiations on Capitol Hill.

“That’s been a top priority for me and my Republican colleagues throughout this debate,” McConnell said. “And it’s been worth the effort. ... Some have suggested that we break that promise as part of this agreement. What [sequestration] showed is that Washington can cut spending. And because of this law, that’s just what we’ve done. ... We’re not going back on this agreement.”

The politics of the budget battle suggest there is little support elsewhere for lifting sequestration, some experts say.

“Looks to me like it’s here to stay,” said Larry Korb, a former assistant secretary of defense under President Reagan and now a senior fellow at the Center for American Progress.

The latest political showdown highlighted the tension between the Republican Party’s traditional defense hawks and the tea party faction that sees a balanced budget as a top priority.

“There is certainly a shifting political landscape that reflects a new fiscal situation and the Defense Department is going to have to adapt to that,” said Pete Hegseth, an Iraq and Afghanistan veteran and Republican who ran for a Senate seat in Minnesota in 2012.

Hegseth now heads up the advocacy group Concerned Veterans for America and is trying to help bridge the divide in the GOP. He said budget pressures have intensified the need to make cost-effective reforms inside the military, such as changes to military retirement, the health care system and the acquisitions process.

Those politically sensitive reforms are backed by most of the Pentagon’s top brass, but are consistently stalled by the lawmakers who ultimately must approve them.

“You can be both a deficit hawk and defense hawk,” Hegseth said. “The way to do that is through reform and to recognize that the Defense Department is going to have to be a part of any reform effort.”

It’s unclear how the government shutdown battle will affect tensions inside the Republican Party, but it may ultimately turn out to be a long-term positive for the military, said Richard Aboulafia, a defense expert with the Teal Group in Virginia.

“If Republicans are sensible, they will quash the tea party and return to a more traditional Republican approach, which is strong on defense. If it is truly a defeat for the tea party, that is good for defense.”